From 0a9e63b8b496d3a5c20098adcd3e136212f6fe9c Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Wed, 5 Feb 2020 10:06:48 +0100
Subject: [PATCH] remove structs from manta task
---
manta.wdl | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/manta.wdl b/manta.wdl
index 38bc196..76c91a6 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -60,8 +60,8 @@ task Somatic {
task Germline {
input {
- IndexedBamFile normalBam
- Reference reference
+ File bamFile
+ File referenceFasta
String runDir
File? callRegions
File? callRegionsIndex
@@ -75,8 +75,8 @@ task Germline {
command {
set -e
configManta.py \
- ~{"--normalBam " + normalBam.file} \
- --referenceFasta ~{reference.fasta} \
+ ~{"--bamFile " + bamFile} \
+ --referenceFasta ~{referenceFasta} \
~{"--callRegions " + callRegions} \
--runDir ~{runDir} \
~{true="--exome" false="" exome}
--
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